| Batch | B002 |
| N Samples | 2 |
| N Pools | 1 |
| N Wells | 11 |
| Batch Control | TRUE |
| B002-P1 Samples | IMM19_698, PB00004-01, PB00006-01 |
| Category | Results | Description |
|---|---|---|
| Well Sequencing and Alignment | Warning | |
| Cell Hashing | Pass | |
| Cell Labeling | Pass | |
| Control Sample | Pass |
The following metrics summarize the sequencing and alignment by 10x well prior to un-hashing and hash-based cell filtering.
| Spec | Median_Range | Inter_Well_CV | Comments | Plot |
|---|---|---|---|---|
| estimated_number_of_cells | 30811 (21882-33097) | 10.0% | Fail: message | |
| fraction_reads_in_cells | 94.0 (93.0-94.9) | 0.6% | ||
| mean_reads_per_cell | 30832 (26087-43885) | 15.0% | ||
| median_genes_per_cell | 1593 (1500-1796) | 4.9% | Warning: message | |
| median_umi_counts_per_cell | 5219 (4848-6153) | 6.8% | ||
| number_of_reads | 946975235 (791967202-1088565134) | 7.5% | ||
| q30_bases_in_barcode | 96.2 (96.1-96.2) | 0.0% | ||
| q30_bases_in_rna_read | 94.3 (93.9-94.7) | 0.3% | ||
| q30_bases_in_sample_index | 94.4 (92.8-95.2) | 0.9% | ||
| q30_bases_in_umi | 96.0 (96.0-96.1) | 0.0% | ||
| reads_mapped_antisense_to_gene | 2.0 (1.8-2.1) | 6.2% | ||
| reads_mapped_confidently_to_exonic_regions | 63.0 (60.1-65.6) | 2.7% | ||
| reads_mapped_confidently_to_genome | 89.9 (88.3-91.4) | 0.9% | ||
| reads_mapped_confidently_to_intergenic_regions | 4.0 (3.8-4.2) | 3.2% | ||
| reads_mapped_confidently_to_intronic_regions | 22.9 (21.1-24.8) | 4.9% | Warning: message | |
| reads_mapped_confidently_to_transcriptome | 58.3 (55.4-61.1) | 3.1% | ||
| reads_mapped_to_genome | 94.2 (92.9-95.5) | 0.7% | ||
| sequencing_saturation | 60.9 (56.0-65.5) | 4.1% | Warning: message | |
| total_genes_detected | 24330 (24169-24554) | 0.5% | Warning: message | |
| valid_barcodes | 97.3 (97.2-97.4) | 0.1% |
| Specification | Value | Comments |
|---|---|---|
| x | x | |
| x | x | |
| x | x | Warning: message |
| x | x | Fail: mesage |
| x | x |
| hto_category | pool_id | n_cells | median_reads | median_umis | median_genes |
|---|---|---|---|---|---|
| doublet | B002-P1 | 76166 | 20637.0 | 7890 | 2209.5 |
| multiplet | B002-P1 | 19143 | 30170.0 | 11515 | 2927.0 |
| no_hash | B002-P1 | 6969 | 8668.0 | 3387 | 1174.0 |
| singlet | B002-P1 | 38770 | 12979.5 | 4889 | 1490.0 |
| doublet | B002-P2 | 72164 | 22688.5 | 7413 | 2076.0 |
| multiplet | B002-P2 | 16543 | 35190.0 | 11448 | 2831.0 |
| no_hash | B002-P2 | 3908 | 4182.0 | 1732 | 566.5 |
## `summarise()` regrouping output by 'hto_barcode', 'pbmc_sample_id', 'sample_hto' (override with `.groups` argument)
| pool_id | well_id | n_cells | median_reads | median_umis | median_genes |
|---|---|---|---|---|---|
| B002-P1 | B002-P1C1W1 | 8721 | 24641.0 | 8200.0 | 2307.0 |
| B002-P1 | B002-P1C1W3 | 13989 | 14785.0 | 5920.0 | 1815.0 |
| B002-P1 | B002-P1C1W4 | 12608 | 15342.5 | 6565.5 | 1964.0 |
| B002-P1 | B002-P1C1W5 | 12351 | 18376.0 | 7195.0 | 2075.0 |
| B002-P1 | B002-P1C1W6 | 13742 | 18716.0 | 6673.0 | 2000.5 |
| B002-P1 | B002-P1C1W7 | 14609 | 15804.0 | 6163.0 | 1890.0 |
| B002-P1 | B002-P1C1W8 | 13344 | 16953.5 | 6399.0 | 1901.0 |
| B002-P1 | B002-P1C2W1 | 12414 | 19354.5 | 7292.5 | 2096.5 |
| B002-P1 | B002-P1C2W2 | 13443 | 18261.0 | 6685.0 | 1944.0 |
| B002-P1 | B002-P1C2W3 | 13556 | 16417.0 | 6203.0 | 1862.0 |
| B002-P1 | B002-P1C2W4 | 12271 | 18944.0 | 6938.0 | 2014.0 |
| B002-P2 | B002-P2C2W5 | 8082 | 22815.0 | 8254.0 | 2280.0 |
| B002-P2 | B002-P2C2W6 | 8323 | 23584.0 | 8009.0 | 2224.0 |
| B002-P2 | B002-P2C2W7 | 7329 | 26043.0 | 8329.0 | 2291.0 |
| B002-P2 | B002-P2C2W8 | 7131 | 26261.0 | 8463.0 | 2308.0 |
| B002-P2 | B002-P2C3W1 | 7092 | 21886.5 | 7456.0 | 2062.0 |
| B002-P2 | B002-P2C3W2 | 7991 | 25453.0 | 8147.0 | 2194.0 |
| B002-P2 | B002-P2C3W3 | 8105 | 23396.0 | 7420.0 | 2060.0 |
| B002-P2 | B002-P2C3W4 | 7715 | 21072.0 | 7047.0 | 1991.0 |
| B002-P2 | B002-P2C3W5 | 7968 | 23740.0 | 7718.0 | 2117.5 |
| B002-P2 | B002-P2C3W6 | 9040 | 22597.5 | 7325.5 | 2063.0 |
| B002-P2 | B002-P2C3W7 | 7427 | 26055.0 | 7729.0 | 2129.0 |
| B002-P2 | B002-P2C3W8 | 6412 | 24037.0 | 7768.0 | 2119.0 |
## Warning: Removed 2 rows containing non-finite values (stat_ydensity).
## Warning: Removed 1 rows containing non-finite values (stat_ydensity).
## Warning: Non-unique features (rownames) present in the input matrix, making
## unique
Batch-level UMAP using 4 principal components (19.4% explained variance).
## Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
## To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
## This message will be shown once per session